Wiki¶

Data location¶

The data was transferred using Globus connect and Ilifu's Globus endpoint from a PC setup in cbio to Ilifu:

/cbio/users/katie/Nono/metagenomics


The data has already been cleaned and decontaminated (human) by BGI, who have also performed a full analysis on the data (see files section)

The full BGI results can be found together with the cleaned reads on Ilifu.

YAMP pipeline update¶

The YAMP pipeline was updated with:

1. the latest metaphlan DB, downloaded from https://zenodo.org/record/4629921#.Yji3YxNBzOR
2. the latest humann DBs (chocophlan and uniref), as described here https://github.com/alesssia/YAMP/wiki/Getting-started#notes-on-the-metaphlan-databases and first downloading the relevant singularity container with singularity pull docker://biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7 The command executed, from within the github directory of the latest YAMP repo was: singularity run biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7 humann_databases --download chocophlan full ./assets/data/chocophlan AND singularity run biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7 humann_databases --download uniref uniref90_diamond ./assets/data/uniref